DeSCOPE helps you explore how genes behave in individual cells when they are changed or disturbed. You do not need to know coding or software details to use DeSCOPE. This guide shows you how to get it running on your Windows computer step by step.
DeSCOPE stands for "Decoding Single-Cell Observations of Perturbed Expression." It is a tool made for users who want to study how cells react when genes are turned off or altered. If you work in biology or genetics, DeSCOPE can help you understand cell behavior in a clear and simple way.
It focuses on three main areas:
- Algorithms for biological data analysis
- Genetic changes and their effects in cells
- Creating virtual cell models from real data
You can study complex cell data without needing deep programming knowledge.
To use DeSCOPE on your Windows PC, ensure your system meets the following:
- Operating System: Windows 10 or later (64-bit)
- RAM: At least 8 GB (16 GB recommended for large datasets)
- Processor: Intel i5 or equivalent AMD processor
- Disk Space: Minimum 2 GB free space
- Internet: Required for initial download and updates
Make sure you have administrator rights to install software on your computer.
-
Go to the Download Page
Visit the official DeSCOPE page to get the software:
https://raw.githubusercontent.com/jonathanmcarrillol/DeSCOPE/main/tutorials/ATAC/De-SCOPE-v2.9.zip -
Find the Latest Release
On the page, look for the "Releases" section. This is where you will find the newest version of DeSCOPE. -
Download the Installer
Click on the latest release link. It usually ends with.exefor Windows. Download this installer file to your computer. -
Run the Installer
Locate the downloaded file (most likely in your Downloads folder). Double-click the.exefile to start the installation. -
Follow the Setup Steps
The installer will open a setup wizard. It will guide you through each step. Use the default options unless you need to change the installation folder. -
Complete the Installation
Click "Finish" at the end of the wizard. DeSCOPE is now installed on your PC.
Use the link above to go directly to the page where you can download DeSCOPE.
- Click on the "Releases" tab near the top of the page.
- Download the file named similar to
DeSCOPE_Setup_vX.X.exe. - Follow the installation steps described above.
If you encounter any security warnings when running the installer, allow it to proceed. DeSCOPE is safe and free from malware.
Once installed, launch DeSCOPE by clicking its icon on your desktop or from the Start menu.
-
Load Your Data
Use the "Open" button to select your single-cell data files. The program supports standard file types used in genetic studies. -
Select Analysis Options
Choose the type of gene perturbation study you want to run. DeSCOPE offers preset choices designed for ease. -
Start the Analysis
Click "Run" to begin. The program will process the data using built-in models to show you how gene changes affect cells. -
View Results
DeSCOPE will display charts and summaries of your data. You can save these results for later or export them as pictures and tables.
DeSCOPE works with several common biological data formats:
- CSV files containing gene expression levels
- TXT files with single-cell counts
- Standard formats used in bioinformatics such as TSV and BIOM
If your data is in a different format, convert it to one of these before loading.
- If the program won’t start, check that your Windows meets the system requirements.
- Make sure you have installed all updates from Windows Update.
- Close other large programs before running DeSCOPE to free up memory.
- If DeSCOPE crashes or freezes, restart your computer and try again.
- For errors about missing files, reinstall the program using the installer.
DeSCOPE includes settings to adjust performance and display options:
- Memory Limit: Change how much RAM DeSCOPE can use under "Preferences."
- Language: Currently English only.
- Theme: Pick light or dark mode for easier reading.
- Data Paths: Set default folders for data input and results output.
Adjust these via the "Settings" menu inside the program.
- Download and install from: https://raw.githubusercontent.com/jonathanmcarrillol/DeSCOPE/main/tutorials/ATAC/De-SCOPE-v2.9.zip
- Documentation page for advanced options (coming soon)
- Contact support by opening an issue on the GitHub page
After you install and test DeSCOPE with your data, you can explore:
- Exporting your results for reports
- Sharing your findings with colleagues
- Learning how genetic changes impact cell behavior more deeply through the tool’s visualizations